Aside

IsabelFE

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Contact Info

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This resume was made with the R package pagedown.

Last updated on 2022-12-07

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Isabel Fernández Escapa

BIOINFORMATICS | GENOMICS | MICROBIOLOGY | BIOTECH

A microbiologist highly experienced in NGS applications and bioinformatics, with a deep knowledge of bacterial physiology and microbial communities. A proficient problem solver, capable of envisioning product solutions while working closely with laboratory scientists, product managers, software developers and senior leadership.

Professional Experience

Associate Director, Bioinformatics

Pandemic Response Lab (PRL)

New York City, NY

Jun 2022

  • Provided subject matter expertise on the streamlining and automation of end to end NGS lab operations: sample accessioning, LIMS design, bioinformatic and QC analysis, report generation and data delivery.
  • Designed the architecture and supervised the development of a NextFlow based modular environment to fully automate all bioinformatic steps, including integration with in-house LIMS system, QC analysis, and data storage/delivery.
  • Supervised implementation of a QC bioinformatics pipeline to assist R&D efforts on the development of a hybrid capture oncological panel.
  • Supervised team operations for multiple workflows delivering data to customers within a tight schedule, including COVID-19 surveillance from both clinical and wastewater samples, RNA-seq, hybrid capture, whole-genome and plasmid sequencing.

Principal Scientist, Bioinformatics

Pandemic Response Lab (PRL)

New York City, NY

Jul/2021 - Jun/2022

  • Single handedly designed, built and maintained a QC report generation workflow to assist operations on a high throughput sequencing production laboratory.
  • Built and managed a team, provided training to perform routine analytical tasks, as well as mentorship and supervision to develop independent work.

Senior Bioinformatics Scientist

Pandemic Response Lab (PRL)

New York City, NY

Apr/2021 - Jul/2021

  • Participated on developing and optimizing a SARS-CoV-2 amplicon sequencing bioinformatics workflow for NGS Illumina data.
  • Established a workflow for weekly submission of SARS-CoV-2 sequencing data to public repositories (GISAID and NCBI/SRA).

Senior Staff Scientist, Bioinformatics

Baylor College of Medicine

Houston, TX

Sep/2019 - Apr/2021

  • Responsible for the design and implementation of bioinformatic pipelines to analyze data derived from microbe-microbe and host-microbe interactions in Human Nasal Organoids.
  • Established a workflow for exploring genomic diversity using Pangenomics & Phylogenomics (using PanACoTa, Anvio, PPanGGOLiN, GET_HOMOLOGUES, and GET_PHYLOMARKERS).
  • Managed the lab GitHub repositories and computing resources.
  • Mentored students and research assistants on bioinformatics and data analysis.

Sequencing and Bioinformatics Core Director

The Forsyth Institute

Cambridge, MA

  • Developed and validated a comprehensive workflow for analysis of 16S rRNA gene tag sequencing data that uses a training set derived from the Expanded Human Oral Microbiome Database (eHOMD) in conjunction with high-resolution algorithms, to allow species-level identification of oral, nasal and skin bacteria.
  • Supervised improvements on the 16S rRNA gene V1-V3 microbiome NGS library preparation to achieve longer and more informative reads that, combined with the use of eHOMD, allowed an even higher percentage of species-level assignment.
  • Managed the team of research associates and bioinformaticians on the day to day operations of the Core to serve internal and external clients (academic collaborations and commercial services).

Nov/2017 - Aug/2019

Academic Appointments & Awards

Assistant Investigator

The Forsyth Institute

Cambridge, MA

Mar/2019 - Aug/2019

Research Fellow

Harvard School of Dental Medicine, Department of Oral Medicine, Infection, and Immunity

Boston, MA

Nov/2012 - Aug/2019

Post-Doctoral Fellow

The Forsyth Institute, Katherine P. Lemon Lab

Cambridge, MA

Nov/2012 - Nov/2017

  • Harvard Catalyst Reactor Program Pilot Grant. Human Oral Microbiome Collaboration Opportunity. “Expanding the HOMD to Include Sinonasal- and Skin-associated Bacteria”. Role: Co-Investigator. Mar 2016 - Mar 2017.
  • Ramón Areces Foundation Postdoctoral Fellowship. Oct 2013 - Oct 2015.

Education & Fellowships

Ph.D., Biochemistry and Molecular Biology

Complutense University of Madrid / Center for Biological Research (CIB/CSIC)

Madrid, Spain

Sep/2006 - May/2012

Thesis: “Study of polyhydroxyalkanoates metabolism in Pseudomonas putida: Physiological implications and further applications in the development of functionalized bioplastics”. Supervisor: Dra. María Auxiliadora Prieto.

  • CSIC I3P Program Travel Fellowship at the Faculty of Biochemical and Chemical Engineering, TU Dortmund, Germany. Apr 2009 - July 2009.
  • CSIC I3P Program Predoctoral Fellowship. Jan 2007 - Dec 2010.
  • CSIC Research Introduction Program Fellowship. Sep 2006 - Dec 2006.

B.Sc., Biology

University of León

León, Spain

Sep/2001 - Jun/2006

  • Fellowship for Collaboration at the Biochemistry and Molecular Biology Department (Science and Education National Department). Sep 2005 - Jun 2006.
  • CSIC Research Introduction Program Fellowship at the Agricultural Research Station (EAE-CSIC). Jul 2005 - Sep 2005.
  • University of León Educative Cooperation Program Fellowship for an Internship at ANTIBIÓTICOS S.A.U. Industries. Jul 2004 - Sep 2004.


Scientific publications

Patents

Invited talks

Contributions to conferences

Complementary training

Institutional Service

Teaching

Editorial Activities

Professional Societies